require("knitr")
knitr::opts_chunk$set(warning=FALSE, message=FALSE, fig.align='center')
library(ggplot2)
library(broom.mixed)
library(broom)
library(tidyverse)
library(tidymodels)
library(plyr)
library(dplyr)
library(plotrix)
library(lubridate)
library(effects)
library(RCurl)
library(chron)
library(lubridate)
library(lme4)
library(emmeans)
library(multcomp)
library(devtools)
library(logihist)
library(popbio)
library(car)
library(lmerTest)
library(cowplot)
library(sjPlot)
library(sjmisc)
library(RgoogleMaps)
library(SDMTools)
library(rgdal)
library(maps)
library(png)
library(ecodist)
library(gridExtra)
Montipora capitata was sampled at four reef locations in Kāne‘ohe Bay, O‘ahu, spanning a latitudinal (north-south) gradient of oceanic input and seawater residence and nearshore proximity (east-west)
We measured changes in total biomass (ash-free dry weight), symbiont densiteis, photopigments (total chlorophylls (a+c2)), and stable isotopes (δ13C, δ15N) of the coral host, its endosymbionts Symbiodinium, and the coral skeleton.
Site map
# attach map GPS data
HI<-readOGR("data/coast_n83.shp", "coast_n83") # in meters
HI <- spTransform(HI, CRS("+proj=longlat +datum=NAD83"))
sites<-read.csv("data/environmental/Reefs_lat_long.csv", header=TRUE, na.string=NA)
# Make figure and export
###############
par(mar=c(1,1,1,1), pty="sq")
plot(HI, xlim=c(-157.86, -157.75), ylim=c(21.42, 21.5), lwd=1, col="gray87")
# adding tick marks and axis lat-long
axis(side=1, at=seq(-157.9, -157.70, 0.05), line=0, tck=0.02, labels=FALSE) # bottom
text(y=21.409, x=seq(-157.9, -157.70, 0.05), labels=seq(-157.9, -157.70, 0.05), cex=0.4)
axis(side=3, at=seq(-157.9, -157.70, 0.05), line=0, tck=0.02, labels=FALSE) # top
axis(side=2, at=seq(21.35, 21.55, 0.05), line=0, tck=0.02, labels=FALSE) # right
text(x=-157.857, y=seq(21.35, 21.55, 0.05), labels=seq(21.35, 21.55, 0.05),cex=0.4)
axis(side=4, at=seq(21.35, 21.55, 0.05), line=0, tck=0.02, labels=FALSE) # left
## add points to map, needs to be 'longitude-latitude formatted'
points(sites[,c(3,2)], pch=21, cex=1.3, col="black", bg="salmon")
text(sites[,c(3,2)], labels=c("SE\npatch reef", "SW\nfringe reef", "NE\npatch reef", "NW\nfringe reef"), pos=c(3,3,1,3), cex=0.5)
par(new=T, mar=c(15,15,1,1))
plot(HI, xlim=c(-158.27, -157.6), ylim=c(21.25, 21.72), lwd=0.4, col="gray", bg="white") # Oahu
rect(-157.87, 21.39, -157.71, 21.53, lwd=0.8)
box()
Figure 1a. Study site locations in Kāne‘ohe Bay on the windward side of the island of O’ahu, Hawai’i
##### save the figure and export to directory? ####
dev.copy(pdf, "figures/environmental/KBaymap.pdf", height=4.6, width=5)
dev.off